Naruto Instrumentalities newest player
by Juubi no ookami
Summary: Adopted From NecroSaintCreed What if Naruto woke up in Tokyo 3. What if he was dragged into a whole new war. What if he was asked to pilot. What if Kurama had died, and what if it all was because he was caught in one final attack on Madara's part. Doujutsu/Naruto Naruto/harem extremely overpowered Naruto Slight crossover later
1. Chapter 1

**Instrumentalities newest player**

**Hello every one Juubi here to bring you my first adopted Naruto and Evangelion crossover story.**

**Recently I had adopted this story from an author known as ****NecroSaintCreed who was unable to complete this story**

An alarm rang throughout the streets of the destroyed suburbs.

"You will not be leaving this warzone alive." "This is for all the things that you've done, You BASTARD!"

Crystal blue eyes flutter open as their owner groggily sits up only to grab his head in pain.

"Just die you Mongrel!"

A young man stumbles down a random street, the sky full of smoke the buildings coming down around him and all he can do is stumble while gripping his head. A Large blast somewhere in the distance causes his unruly blonde hair to billow in the wind, as his ragged looking clothes barely cling to his figure.

"How does it feel to know I killed all those you held precious to you? Do you feel Angry? I am going to kill you!"

"Prepare for launch!" Lieutenant Colonel Misato Katsuragi commanded as she was given the confirmation that the young Shinji Ikari could successfully pilot Unit-01.

"Preparing for launch." a male voice responded over the intercom. "Lieutenant, there is a strange energy reading on the ground of Tokyo-3, its 300 kilometers from the south entrance." one of the people at the computers reported bringing the image onto the larger screen.

"What is it?" She asked fearing that it may be yet another angel. "I can't rightfully tell you, but what I do know is that it's something we might want to fear more than our current angel." the man reported.

"Try and bring up any remaining cameras in that sector."

"You may have one boy but you'll die before I will. KAMUI… Shinken"

Everyone in Nerv HQ watched as the blonde suddenly cradled his as if he was in agonizing pain, momentarily forgetting about Shinji as he was launched even the angel ignored him as it to noticed the dramatic increase in power.

"Lieutenant the readings have double-no tripled in a matter of seconds." the man from before said with his jaw seemingly slack from astonishment.

Then there was a sudden stillness that seemed to cause everyone to catch their breath as the boy stopped moving, completely. They knew he was still alive oh they knew the numbers were still climbing to tremendous heights.

"Kurama?" the young blonde asked himself in search of that annoying, but comforting voice he knew was in his head. "Kurama?!" he said as he felt himself get desperate. He knew that the damn fox was still there he had to be, Right?

'No, all I've known it can't be gone. One friend... please just one friend.' he thought desperately as he followed the endless trail of chakra that always lead him to the overgrown fur ball. 'Kurama answer me!?" He thought.

"No…" the blondes hollow words rang throughout the entire city. Again they watched as they quite clearly heard his words. The silence was so physically unbearable, it was attacked the very souls of anyone watching.

They watched as the wind began to suddenly pick up as if it was originating from the blonde boy himself, which they quickly found out it was, as the young man started screaming in a fit demonic rage and sorrow. It was so physically unbelievable to them that were till their sensors started to explode.

"Lieutenant Sensors are down in all nearby sectors." "Activate the far ranged sensors and keep them locked." she responded not taking her eyes off the young man crying tears of blood, his eyes had gone from crystal blue to a deep amethyst purple with a single gold ring out-lining it and three back to back crescent moons.

"NOOOOOOOO!" it was magnificent the amount of power the boy held, without even remotely doing anything it still destroyed the landscape around him. In his eyes one could see so much untamed anger, so much rage, so much sorrow all of it; and in his eyes one could see that it needed release.

Sadly for the angel no matter the distance between the two of them at that moment, it had inadvertently locked eyes with him and in a single glance sealed its fate as the world's biggest punching bag.

He was gone in a literal flash one, leaving no physical evidence of him ever being there well besides the collateral damage to the surrounding area. Everyone in the headquarters was gob smacked some even thought they saw Gendo Ikari's glasses fall off his face, though they were never heard from again for what they witnessed. Misato was the first one to recover and was instantly giving out orders.

"Locate him now!"

"We already have." "Where is he?" "Sector 7"

"But that would mean..." "Bring up the Angel NOW!" Gendo declared as he took this as a moment to step in.

What they saw when they brought it up on screen was nothing but reformed insanity.

They brought the camera up in time to watch the blonde basically back hand the angel clear across the city, for the next five minutes was the largest single player game of volley ball ever recorded in history and all anyone could hope to catch of either the 'ball' and the blonde was mere blurs.

What was once going to be a supreme battle for human existence became a quick one sided slaughter fest and serious anger management issues.

When it finally stopped the blonde looked like he was barely breathing hard while the angel was trying to crawl away. "Trying to crawl away" the blonde said his eyebrow twitching violently as he reached out and grabbed the angel by the leg

"Where do you think you're going…? I'm not through with you yet!" the blonde yelled as he yanked the angel back towards him ripping the leg clean off as he leaped into the air. The camera's barely caught the strange swirling sphere of energy as he brought it down upon the core of the angel.

Any hopes of seeing the results of the blonde's demonic beat down were lost as the shock wave destroyed every camera in the area.

"Give me a status report on the Angel condition!" Gendo called out as he looked down at the first person who gave him an answer.

"Nothing sir, it's like its very existence was erased from reality,-" someone called out pausing for a moment. "Sir the superior energy signature is fading fast."

Suddenly, they all saw Naruto once again but this time he was seen with something in his mouth. The other members of Nerv all watched in horror as the child dug into the core of the now dead angel.

"Is… is that the S2 engine he is devouring?" Gendo asks in shock that a normal human could ingest an organ that was supposed to be located within the core of an angel.

Naruto's body than began to glow just like Adam and he huge a halo for about two seconds before the light died down and he was seen on the ground unconscious.

For about five minutes no one at Nerv that had watched the massacre of the greatest threat that humanity has ever faced.

Without even a moment's hesitation Gendo had his plan devised, "Lieutenant have Shinji's new task be to safely retrieve the young man."

(Next morning)

Once again Crystal blue eyes snapped open to their least favorite sight, one which was confirmed when the smell of anesthetic and chemicals hit his nose, and the silence that always seemed to follow as if one was in a library of the sick.

He had successfully found himself once again in a hospital room. "Way to go with that one." He said to himself as he went to sit up only to find his arms restrained. "I see you're awake." A feminine voice spoke drawing his attention to the corner of the room.

There sitting in the chair was Lieutenant Colonel Misato Katsuragi a gun in hand in case anything went wrong, "We'll release you as soon as you tell us who you are and where you came from." She told him slightly sweating as he only gave her a blank stare.

"My name is Naruto Uzumaki-Namikaze, and my question is who tied me down?" he asked again with his stoic expression Causing her to feel a little bit of hesitance, believing that he was most likely going to take hostile action to being restrained she raised her gun and took the blame.

"I tied you down then allowed the doctors to take care of your bruises." she said ready for any sudden moves on his part only to face fault at his reply.

"You don't really look like the type that would be in to bondage..." he stated in a matter of fact tone before adopting a rather distant look.

"WHO THE HELL DO YOU THINK YOU ARE BRINGING MY SEX LIFE INTO THIS!" she yelled at him recreating his first sensei's famous jutsu, scaring him a little on the inside due to know one ever figuring out how he actually made said jutsu.

"And what if I was into to bondage not saying I am but what if I was then what would you do you cheeky brat." she said with a grin thinking she caught him at his own game, completely forgetting the reason she was here I remind you, only for it to drop when he responded with a mischievous little smirk of his own.

"This."

And in a puff of smoke they had seemingly switched places.

"Now I guess I'll be off." he said suddenly wearing all his clothes from before without the blood dirt and grime they had when they were taken from his form.

"You can't just leave me here!" she demanded after getting over the whole switching places thing. Her only response was to have a rag shoved into her mouth, and a stern look from the now named Naruto.

"Now if you were into, and I'm not saying you are bondage you would enjoy this." he said as he left poor Misato tied up with a heavy blush upon her cheeks.

It wasn't long before he found himself walking down a random hall way that he took on instinct believing it as his way out only to feel himself freeze as not even a moment later one other person turned down that very same hallway.

The person in question was a teenage girl with blue hair that was wrapped up in bandages and also covered one of her eyes. She had on a very strange bodysuit on that seemed to compliment her womanly figure.

She had a cast on her arm that was held up in a sling. Naruto then looked into her eyes and noticed that she was a bitterly unhappy young woman that seemed to have his huge sense of negative self-worth.

As for Rei she stared at the ninja finding him strange and very interesting. She had seen what the man had done to the angel without the strength of an eva and it peeked her curiosity.

Looking over his appearance, Rei found the mysterious child very pleasing to the eyes and she found that she was curious about the lines on his face.

Rei then studied his clothing and she found his choice of attire while a little strange seemed to suit him nicely.

Finally, Rei looked into Naruto's eyes and she was able to sense an overwhelming presence of pain, loneliness and despair.

It surprised her as he seemed to be this all power entity and yet seemed to have experience so much sorrow that it surpassed all of what she experience.

"Who are you… what is your name?" Rei asked in an emotionless tone of voice that causing Naruto to offer her a sad smile.

"I am someone who has lost everything he once held dear." Naruto said as the sorrow that Naruto sensed in her underlined despair in her words.

It was the sound of someone who believe that they are expendable and truly believe they were not human.

Suddenly, Rei clinched her head and her arm in pain and begins to fall only to be caught by Naruto.

"Hey are you alright?" Naruto asked as he held her so that she didn't hit the floor. Opening her eye and reached out with her good hand in an attempt to grab a hold to something that would help her stand up.

"Hey, relax you don't need to waste any more energy." Naruto told her as he picked her up bridal style.

'She's in a lot of physical pain however it's nothing compared to the pain I see in her eyes… however what I really want to know is why she smells so strongly of blood.'

**(Elsewhere in Nerv headquarters)**

Gendo Ikari watched Naruto's interaction with Rei though one of the cameras. "Hm… So, Rei has taken an interest in our guest Gendo." Kozo Fuyutsuki Gendo's right hand man said. As they watched Naruto run through Nerv carrying Rei.

"So it would appear." Gendo said as he stood up and walked out of the room with Kozo following right after the man.

"The child had suddenly appeared out of a rift in space during the third angel's attack." Gendo said as walked through the halls of Nerv.

"The boy than starts to generate an extraordinary amount of energy that was able to negate the Angel's AT field with ease." The boy then unleashes a primal scream and proceeds to single-headedly destroy Sachiel." Gendo said as they listened to the shouts of the other to find the escapee.

"After he was done with the Angel he began devouring the core and started to enter an "awaken state for a few seconds before losing consciousness." Gendo finished as they heard the guards shout out that they found him and that he was staying to escape while holding the first child hostage.

"They sure are having a hard time." Fuyutsuki comments as they headed to where Gendo believed they would end up.

"What we have here could finally be our key to achieving the plan for Human instrumentality, and this time I will use everything at my disposal to see that my plans succeed, I will even use that child if I need to." Gendo states as thoughts of his wife Yui Ikari who had assimilated with Eva unit one.

**(With Naruto and Rei)**

Naruto sighed has he ran around Nerv headquarters with Rei still in his arms. Naruto had decided to take her to the same hospital room that he had woke up in that day.

This proved to be a bad idea on his part since he forgot that he had left some woman there tied up when he escaped. According to Rei that women was the operations director of Nerv Misato Katsuragi.

When he was about to turn down the hall when she appeared with twenty guards surrounding her and she looked both extremely embarrassed and royally piss.

"I want you to capture that brat and make sure to chain him down." Misato commanded as the guards started to close in on them.

"Sorry to disappoint you sweetheart but I'm not into all of that kinky stuff." Naruto said before disappearing in a swirl of leaves."

And so here they two where, the first child and the Sage of six path on the run from humanities last hope of defense. After about twenty minutes of dodging the guards Naruto and Rei finally came to where the Evas where being held.

Naruto gently laid Rei on a hospital bed that had been left there and placed a seal on the door to keep the guards out until he was finished helping Rei.

"That should hold them off for a while and give me enough time to heal you." Naruto said as he his hands started to glow green.

Rei who was still in pain opening her face and stared at Naruto's hand warily. "What do you intend to do." Rei asked not understanding way his hands where glowing green.

"Oh this is a healing technique that I've learned from an old friend of mine." Naruto explained to Rei as he placed his hands on her cast. Rei let out a sigh as Naruto worked his chakra into her. Rei could feel Naruto's energy flow through her arm.

As he worked on her arm Naruto found that he was able to use this jutsu a lot more easily than he could before the war. 'Those where the good old days.' Naruto thought as he finished Rei's arm.

Naruto then got to work on her eye. "So can you feel me in on what that thing over there is?" Naruto asked the first child.

"That is the evangelion… humanities last hope for survival." Gendo Ikari said as he made himself known with Fuyutsuki right beside him. "Who the fuck are you." Naruto said as Rei sat up.

"He is Nerv's commander Gendo Ikari, he's is the man who devote everything to this organization." She said which Naruto responded to by rolling his eyes.

"You've caused quite the commotion, so may we know the name of the man who destroyed an angel." Gendo said getting a weird look from Naruto.

"My name is Naruto Uzumaki-Namikaze and wait a minute… so you're telling me that the creature I just killed was an angel... what the hell did you guys do to get on Kami's hit list" Naruto asked as Rei began to take off her bandages.

"Mankind is on the verge of extinction and our only hope is the evangelion that are piloted by Rei and my son Shinji however, they lack experience and will likely get themselves killed and then that will be the end of humanity." Nerv's commander explained.

"So I ask you, the fallen Angel Naruto Namikaze will you fight for humanity's future?" Gendo asked Naruto. Naruto just stared at Gendo with a look that was devoid of emotion. While Naruto was giving Gendo a blank stare, Naruto mind was a maelstrom of emotions.

On one hand, Naruto could read the man like an open book and could tell that he was planning to use Naruto for to accomplish his on goals even if that meant sacrificing him in the process.

'I could just tell him to fuck off and leave, it not as if this guy can stop me.' Naruto thought as he activated to Rinnegan only to be stopped by Rei who stood before him.

"My name is Rei Ayanami, I look forward to working with you." Rei said as she gave Naruto a short bow, getting a smile from Naruto.

'Well I guess I can humor him until I find out where the hell that bastard sent me.' Naruto thought as he decided to lay some ground rules.

If you want my help there are a few conditions of mine that needs to be met." Naruto said as he suddenly vanishes only to appear right beside Gendo and Fuyutsuki. This caused Fuyutsuki to jump in surprise and got Gendo to sweat a little.

These conditions must be met or I leave here right now and trust me when I say that nothing you do can stop me." Naruto said as he unleashed one percent of his power which, was enough to cause Fuyutsuki to almost have a heart attack.

"And just what are these conditions." Gendo asked as he tried his best to keep from having a mental breakdown as he stared into Naruto's purple ringed eyes.

Rei having been dragged by Naruto when he appeared beside Gendo, found that she was a little dizzy and was having trouble not falling over. Seeing this Naruto helped support her so that she didn't fall on her face.

Suddenly Misato and a group of guards enter the room that they were in. Commander there is something wrong with the door to the… there he is, commander get away from him." Misato said as she and the guards try to close in on Naruto.

Before they could get to close, chains erupted out to the floor, creating a wall between them. "The grown-ups are talking right now, Misato-chan so, I don't you be a good little girl and stay quiet." Naruto said as he turn his attention back to Gendo.

"Stand down Lieutenant colonel Misato Katsuragi, we are merely trying to come to an agreement." Gendo said confusing the woman.

"My first condition is rather simple, I will need all the information that you have on these angels, and all new information that you will be obtaining, and you will give me that information to me right away, and if you try to lie to me I will find out and you will be dealing with this." Naruto said as a giant demon head arose out of the floor scaring everyone within the room.

"What the hell is that thing?!" One of the guards yells out in fear much to Naruto's amusement. Rei stared at the creature in curiosity as she wondered if it was a creature similar to the angles and then she looked towards Naruto with a questioning glaze.

"Everyone I would like you all to meet the King of Hell, his job is to tell me if someone is lying to me about important information and he will rip your souls from your body." Naruto explained with a happy smile on his face.

Suddenly, Misato and the guards all pulled out guns and began to open fire on the king of hell. This however proved to be useless and the bullets were halted in midair and then fell to the floor harmlessly.

"Oh and just so you know, he is an immortal demon and you can't even touch him with any weapon and even an explosion that can take out an entire city." Naruto explained as Rei reach out to touch it.

"I… see… and what of your other conditions?" Gendo asked just wanting to get this day over with and return to the commander's office.

"Right then, my second condition is that you provide me a place to stay preferably one close to my partners Rei and this Shinji kid, I've got it you get us a place with enough room for all three of use to live in." Naruto said confusing Rei.

"Why would you request for us to live under the same roof, how would that benefit you?" Rei asked Naruto, finding herself curious about the strange condition. Suddenly the king of hell disappeared before Rei could touch it.

"Oh I get it, with you three living together you are hoping to form a bond and promote teamwork." Misato said since she had once thought of that idea before but had decided against it.

"While the might be the best way, I don't think that it's right for two boys and one girl to be willing together… I mean who's to stop you from taking advantage of poor Rei here…?" Misato asked with a smug look on her face.

"Well then why not live with in acting as their guardian." Fuyutsuki suggests much to Misato's dismay. "That's an excellent idea Fuyutsuki, it will be your responsibility to make sure that there will be no problems between the children." Gendo commanded much to Misato's dismay.

"Yeah sir," Misato said as she hung her head in defeat. "Now then, the last thing I will need are weapons, preferably two sword strong enough to cut through an angel." Naruto said getting a nod from Gendo.

"I believe that we are done here, Misato take Naruto, Rei and Shinji out to get something to eat or something while you're living arrangement are set up." Gendo said as he and Fuyutsuki left.

"So then, who wants ramon for lunch?" Naruto asked getting a surprised look from Misato, and a curious look from Rei.

**END**

Well there it is the first chapter. I hope that you guys all enjoyed this story.

I would like to once again thank NecroSaintCreed for this story.

Ok this story is A Naruto x Rei x Mari x Misato and Shinji x Asuka

This is the Characters' Ages

Naruto- 17

Rei- 16

Mari-16

Shinji- 15

Asuka- 15

Starting next month I will be starting college so I will only have time to work on at least two stories each month.

The three stories I will be working on next month will be Naruto Sekirei chronicles Naruto the devil prince of Jurai and Naruto the prince of the Demon world.

The month after that I will be working on Naruto Sekirei chronicles, Instrumentalities newest player and Naruto/Gaara Locked in the undead Apocalypse.

This will start on the twenty-fourth so before then I will be working on each story as much as I can before then, so expect a chapter every one-two days for one of my stories.

The Rei Ayanami I will be using has is the one from the Eva manga Gakuren Datenroku. This means that while still somewhat gloomy and distant she will be a lot more expressive with her emotions and will respond more to Naruto.

Mari will of be her Rebuild movie self.

Shinji and Asuka will be the Rebuild movies versions.

All the Eva's will be the Rebuild versions and I will be also using the some of the random angels

Make sure to read, follow, review and Subscribe as always and I will see you guy next time

Juubi out


	2. Chapter 2

**Naruto Instrumentalities newest player Chapter 2**

Ladies and gentle Welcome, Juubi is here bringing to you the second installment of Naruto Instrumentalities newest player.

I am happy to say that the first chapter was a huge success and that I will be doing everything I can to keep its success going.

Parings for this story

Naruto x Rei x Mari x Misato

Shinji x Asuka

**(Previously)**

"Well then, why not live with them, acting as their guardian." Fuyutsuki suggests much to Misato's dismay. "That's an excellent idea Fuyutsuki, it will be your responsibility to make sure that there will be no problems between the children." Gendo commanded much to Misato's dismay.

"Yeah sir," Misato said as she hung her head in defeat. "Now then, the last thing I will need are weapons, preferably two sword strong enough to cut through an angel." Naruto said getting a nod from Gendo.

"I believe that we are done here, Misato take Naruto, Rei and Shinji out to get something to eat or something while you're living arrangement are set up." Gendo said as he and Fuyutsuki left.

"So then, who wants ramon for lunch?" Naruto asked getting a surprised look from Misato, and a curious look from Rei.

**(With Naruto and the others)**

"Well, here we are." said Misato as she opened the door to their new home. The place was a three bed room, two bathroom apartment. The master bed room was at the end of the hall and it had its own bathroom.

Rei walked into the apartment, Naruto then walked in right after her. "Well come on in Shinji." Misato said while Naruto and Rei turned their attention to them.

"Um… I don't want to intrude." Shinji said, feeling a little unsure about staying there. "What are you talking about, this is your home just as much as it is ours." Naruto said to Shinji, getting Shinji's attention.

"I personally asked for this place for the three of us to stay, the only one who could be intruding is Misato." Naruto said much to Misato's annoyance. "Hey! How am I the one who's intruding?" Misato asked as she and Naruto started arguing.

'Those two have been arguing all day and the only time they stopped, was when Naruto decided to focus all of his attention on Rei, who had also been paying close attention to him.' Shinji thought.

However before they could start, Shinji walked past the door and closed it. "I'm… home." Shinji said, getting a smile from Misato and a grin from Naruto. "Welcome home Shinji-kun." Misato said while Naruto turned to Rei.

So after figuring out who gets what room and who does the chores on which day. After that Naruto decided that it was time to give an old school team introduction.

"Okay, so it's time for us to do a proper introduction." Naruto said, causing the others to stare at him with a confused look on their face. "What do you mean by proper introduction?" Rei asked the young sage.

"I mean tell us your names, like, dislikes, and goals for the future." Naruto explained the simple concept to them.

"This is an exercise that I did back in my world when I got my first team, which I will explain in a moment.

"My name is Naruto Uzumaki Namikaze, I am a Shinobi from a village known as Konoha and am it's former leader." Naruto said surprising the others.

"AS of now the only people who I like are you three and I dislikes are people who can't blame others for the sins of someone else, just because it's convenient to blame them." Naruto said confusing Rei, Misato and Shinji.

"My hopes for the future is to kill all Angels so I can live a normal life." Naruto finished before addressing Misato. "You, lady with the S&M fetish, it's your turn." Naruto said, with a grin on his face much to Misato's dismay.

"My name is Misato Katsuragi, I am twenty-nine years old and a lieutenant Colonel at NERV." Misato began. "I am the field commander for the Eva pilots and I handle many bureaucratic aspects for NERV."

"My likes are Shinji-kun, Rei, Naruto-kun, Ritsuko and Pen-Pen." Misato said confusion Naruto. 'Who the fuck is Pen-Pen.' "My dislikes are two men who shall not be named, Naruto and Ritsuko." Misato said confusing Naruto and Shinji even more when she said that she liked and disliked Ritsuko and Naruto.

"I hope for the future is to become a Captain and to defeat the angels, while keeping you kids alive." Misato said, finishing her introduction.

"Okay, now Shinji it's your turn." Naruto said causing Shinji to jump. "Oh um… My name is Shinji Ikari, I am fifteen years old." Shinji said before continuing. "My likes so far are you guys, I guess and I dislike my father."

My goal is… actually I don't really have one." Shinji states causing Naruto to frown. 'Ok so the whole dislike of his father is only partly true and by the look of it, the boy afraid of getting hurt by others,' Misato and Naruto thought.

They noticed how hesitant Shinji seemed when speaking and the fact that he was very uncomfortable around them.

"Okay now it's time for the beautiful Rei Ayanami our Moe-inspired female protagonist's introduction." Naruto said in a dramatic way causing both Misato and Shinji to gain sweat-drops on the back of their heads.

"My name is Rei Ayanami, I am interested in Naruto and I am loyal to NERV." Rei said, her voice lacking emotion and her face expressionless, something that seemed to irritate Naruto. "I goal for the future is to eliminate all angels and to find out more about humanity." Rei said.

'So, we have a two individuals who are broken beyond repair, and a girl who has never learned how to express human emotion huh… this is going to be a pain in the ass.' Naruto thought knowing that everyone was probably going to go through some hardships.

"Well now that that's out of the way, why don't you two go take a bath, you two smell like blood." Naruto said. Starting tomorrow we will be am official team.

Rei why don't you use my bath while Shinji uses the other bath." Naruto suggested, as Rei stood up from the table and walked you the master bedroom. "I guess I'll use the other one then." Shinji said as he walked to the bathroom.

"Why do you get the master bedroom?" Misato whined, as Naruto flashed her a grin. "Because this is my house." Naruto said, causing Misato to grumble about disrespectful blonde-haired brats.

"AHHH! Naruto, Misato there… is… um… a thing." Shinji said frantically, confusing both the two. Suddenly, a penguin walked out from the bathroom. "Oh, that thing, actually he is a warm-water penguin, his name is Pen-Pen." Misato told him.

"Squawk!" Pen-Pen said hold up his claws at Naruto. "What's sup bird, how's it hanging?" Naruto asked Pen-Pen. "Squawk!" Pen-Pen said before opening a small compartment inside the refrigerator.

Pen-Pen gave Shinji a look, before walking into the compartment and closing the small door. "Since when do birds like that even exist?" Shinji asked Misato who didn't see what the big deal was about it.

"Since always I guess, but they are rare now a days, though I guess I should have mention he was going to be living with us." Misato said.

"Well, now that that's out of the way, don't you think you should cover up?" Naruto said with as he took a swig of Misato's beer, while Shinji covered himself and ran back into the bathroom.

"Hey what the… that's mine you jerk." Misato said as she tried snatching the beer can out of Naruto's hand, only for Naruto to move the can out of her reach by leaning back in his chair.

"I know, I just want to try it." Naruto said before drinking a little more and then giving it back to Misato.

"I hope you didn't backwash." Misato said as Naruto gave her a smile.

**(Ritsuko and Gendo)**

"How did Rei seem this afternoon?" Ritsuko asked as Gendo stared at Unit 0. "You went to see her after she got out of the hospital didn't you?" Ritsuko asked Gendo, feeling upset that the man was neglecting Shinji.

"She's with the boy and my son in their new residents." Gendo told Ritsuko who had been taking care of some top secret research. "Wait, wasn't she really injured not too long ago?" Ritsuko asked her boss.

"It would appear that the boy, Naruto Namikaze had healing abilities that far surpassed anything that science could and had her injuries healed in a matter of seconds." Gendo informed Ritsuko much to her surprise.

"He healed her, but how?" Ritsuko asked, surprised that someone could fix broken bones and slightly damages internal organs.

"You should ask him tomorrow yourself Ritsuko, however this will proved to be useful if we can ran a few more tests on him… by the way what did you find after getting a blood sample from him?" Gendo asked the woman who sighed in defeat.

"The blood test only proves that he is a completely normal human male." Ritsuko said, causing Gendo to turn towards her with a surprised look on his face, although his shades did a great job of concealing this.

"That can't be, you're telling me that the test came back saying that there is nothing abnormal about him at all?" Gendo asked. "The only thing that I was able to learn is that his body is somehow perfect." Ritsuko said, causing Gendo to stare at her in confusion.

"What do you mean perfect, how is it perfect?" Gendo asked finding this information very interesting. "What I mean is, Naruto's body seems to be flawless in every sense of the word, he can't contract any diseases as his antibodies seemed to be able to kill any foreign invasion." Ritsuko said.

"He also seems to lack an AT-field." Ritsuko informed Gendo, who by now had beads of sweat rolling down his neck. "Is there any way we can use this on other humans it we mix his DNA with them?" Gendo asked referring to Naruto's blood.

"I'm afraid that's impossible, as for some reason it rejects everything that doesn't have his blood-type and Naruto's blood-type is actually a type not known in history.

"A new blood-type?" Gendo said to himself as he turned back to look at Unit 0. "Ritsuko, I want you to continue your research at a later date." Gendo said as he thought of different ways he could obtain more information on Naruto.

"What about your son? Psychologically speaking, he seems rather unstable." Ritsuko said, hoping that Gendo would do something about it. "Let him be, if nothing else it will give us an excuse to bring unit 0 out of suspension."

Then we will act in accordance with lieutenant Katsuragi's suggestion." Ritsuko states.

As the two talked about the other matters, they never noticed the pair of eyes that where lingering in the shadows of the room they were in."

**(With Naruto)**

"So, the only thing they could find from the tests was that I'm completely human huh." Naruto states in amusement. Naruto was sitting in his room on his bed watching Gendo and Ritsuko from the Rinnegan eyes of one of his clones that he had made follow Gendo all day.

"That's good as it would mean that the seals I have placed on my body are still working at 100% efficiently." Naruto said as he cut the link between him and the clone, knowing that anything it learns while watching Gendo he would learn after it dispels.

'I refused to be use by someone like that fool, I can't believe that he neglects his own son, it's unforgivable… Ritsuko however, seemed to be generally concerned about Shinji.' Naruto thought.

"I wonder if I could "Persuaded" her into joining my side… If I decide to do a hostile takeover of NERV after I learn what that man is really up to." Naruto thought as he started thinking of plans he might need if he decided that he should bring her to his side, since he found that she could be a great ally and friend.

After thinking for five minutes, Naruto sighs and does a hand-sign. A seal appeared on the back of his hand and started to glow bluish-green. A small rip in space appeared before him and Naruto reach in and pulled out a small box.

Once Naruto opened the box, he pulled out a picture of three girls that look around his age. The first, was a woman who had short black hair and was wearing a black kimono with white trimmings.

She was holding a small pink pig and her eyes were closed, while she had a goofy smile on her face. This was Naruto's third fiancée Shizune.

The next girl who was on the right side was a beautiful women with long black hair and had fair-skin. She was wearing a royal kimono from the land of snow and she had her eyes closed, while a calming smile on her face. This was Naruto's second fiancée Koyuki Kazahana.

"The girl in the middle had dark blue hair and fair skin. She had a more well-endowed body and had lavender eyes. She had a timid and kind smile on her face and she was wearing a white kimono that had an autumn leaves design on it.

This was his first wife Hinata Hyūga. Naruto smiled a sad smile as he looked at the picture. 'Those where happier days.' Naruto thought.

"However, it all came to an end the day Obito killed them and everyone who fought against him and Madara." Naruto said to himself as he look towards the moon outside his window.

**(Misato)**

Misato sighed in contempt as she sat in the warm water of the bathtub. As she soaked, she started to think about the events of the last two days. 'Naruto Namikaze, age 17, everything else about him is unknown.' Misato thought.

'Has the ability to fight an angel without an AT-field or an Eva… he has also devoured the core of angel.' "Where did he come from and better yet who sent him to this world.' Misato thought as her thoughts wondered to Shinji's situation.

'The third child, he was suddenly selected without a preliminary report.' 'Also there's the timing of the angel attack, it was the same day he was scheduled to arrive.' Misato thought.

'Not only that but, the fact that he's commander Ikari's son, the coincidence just keeps stacking up, yet we did defeat the angel so that has to count for something.' Misato thought as she sighed and stared up at the ceiling.

"But I still don't like it."

**(Shinji)**

'Another ceiling that I don't recognize… I guess that's no surprise, there's no place in this entire city I'm familiar with.' Shinji thought as what Naruto and Misato had told him at the door ran through his mind.

'Why am I here?' Shinji asks himself only for images of Sachiel to enter his mind.

'The angels.'

**(The next day)**

Misato, Naruto, Rei and Shinji where back at NERV. Shinji was put through a shooting simulation that, would train him in utilizes his Eva's gun properly and also work on his aiming. This simulation was a program that was built into the entry plugs computer system.

"Ritsuko told him to keep doing it until he could do it almost perfectly.

Misato had been charged with handing Naruto a pamphlet at gave him the run down on what NERV did and all that stuff that Naruto had learned already, thanks to his clones that he had concealed all round NERV.

Naruto was then taken by Fuyutsuki to a room, to test out some of the weapons that they were making for him. "So, what have you got for me, old man?" Naruto asked Gendo's right hand man. "We have made for you, weapons that are similar to the ones issued for the Eva." Kozo tells Naruto.

"First on our list is the twin master vibration swords or MVS for short." Fuyutsuki explained to Naruto as the twin grey swords. (Think Lancelot Albion's twin blades.) "Now these are incredible, twin swords with the ability to vibrate at an extremely high frequency." Naruto said as he picks up the twin blades. "They are surprisingly very light for weapon that you claim are similar to the ones used by Evas." Naruto said as the twin blade began turning red. "Light? Those two swords alone took an Eva to move." Fuyutsuki said causing Naruto to stare at him.

"If it took and Eva to lift then how did you get it here, both Eva pilots where with me the entire time?" Naruto asked. We used the same machine we used to put the Eva together." Fuyutsuki states.

The system has your blood that we got a sample of after you killed the angel Sachiel, and we've also matched it to your brain-waves that we calculated while you were unconscious." Fuyutsuki explains to Naruto.

"This is very good work, I have another request for you." Naruto said as he hands Fuyutsuki blue prints for a weapon. "Do you think you can create two dozen of these kunai?" Naruto asked Fuyutsuki who studied the blue prints.

"I could have these done in no time actually, however I don't think I will be proficient against and angel." Kozo said only for Naruto to smirk. "We will see." Naruto said cryptically, confusing Kozo.

Suddenly, the alarms that signaled an angel attack turned on letting them now that the fourth angel had come.

"I guess it's time, old man I'm off.

**(NERV Command Center)**

"We have a confirmed visual on the object." "The target has been verified." The members of Nerv's combat sector. "Analysis pattern blue, it's here the fourth angel Shamshel." Ritsuko states as they see the angel head towards them.

Shamshel was an insect-like angel with segmented arms, mouth with mandibles and "fangs", and an exposed spine in the thoracic cavity to which ten legs attach. (Rebuild version)

"Now battle stations condition one." Misato commands her subordinates

"Roger that, preparing city for ground to air interception." Makoto Hyūga said. "Unit 1, transitioning to battle configuration." Maya Ibuki states.

NERV sounds the alarms and then puts the entire city on lock down. All civilians were sent to shelters, the building went underground. Gun torrents started rising from the ground, along with other equipment.

"Transition complete, central dogma districts 1-7 have been retracted." "Government ministry have been notified, target is continuing its advance.

"What is the status of all civilians?" Misato asked Shigeru Aoba. "So far all districts have reported successful evacuations." The man informed her.

Suddenly, the Japanese government opened fire on Shamshel using the gun torrents, which had no effect on the angel.

The Japanese government, just requested that the Eva mobilization." Aoba tells Misato as he hangs up the phone.

"They just don't get it do they, we will mobilize whether they like it or not." Misato states.

**(The battle with the fifth angel)**

"LCL charged, crypt lock released." 'Dad isn't even watching, so why am I even piloting this thing again.' Shinji thought as an image of Naruto and Rei appeared in his head.

'I do it because, Naruto and Rei are fighting as well, and I do it because they acknowledge me right?' Shinji asked himself, as he got ready to launch.

As Shamshel came within range, Shinji in Eva unit one was launched to the surface. "Center the gun to the target's weak point and pull the trigger." Shinji started to Chant to himself.

"Alright, let's just try to do as we practice okay Shinji." Ritsuko said as Shinji turned to face Shamshel and shoot at it with a hug machine gun. The bullets all were blocked by Shamshel's AT-Field much to Shinji's annoyance.

"Check your fire or you will lose the target in the blast cloud." Misato told Shinji as he unloaded the shells, allowing them to fall to the ground, destroying a few cars in the process.

Once he ran out of bullets, Shamshel's energy tentacles lashed out at him from behind the smoke. Eva unit one was forced on his back as the tentacles almost cleaved it in two.

"We are sending out a spare rifle." Misato informs Shinji as Nerv uses the launcher to send the rifle and Misato commanded him to take it. This however wasn't happening as Shinji was a little shaken up by Shamshel's attack.

Seeing that his enemy was unable to move right now, Shamshel slowly advances towards Shinji while it's moves its segmented arms and legs, making an annoying crackling sounds.

"Shinji stared at the angel in horror as its energy tentacles lash out at him once again. Shinji dodged the tentacles the first time, only to get hit by them the second time and sent flying into another building as the buildings around them were cut in two.

Shamshel then knocked Shinji through that building which knocked out his battery cable. "Umbilical Cable has been severed, switching to internal power." Makoto proclaims. "Operational time four minutes and fifty-three seconds." Maya states as Misato stares at the battle with a horrified look on her face.

Shamshel wrapped his energy tentacle around Eva unit one's leg. The angel then lifts the Eva into the air, before throwing unit one into a hill. "Shinji are you alright… Shinji!" Misato calls out the boy's name. Shinji however was unable to respond do to the fact that he was a little dazed.

"What's the damage?" Misato asked her subordinates. "None all combat operations are normal." said Makoto, as Shinji finally shook off his dizziness. Shinji then noticed that there were two teenage boys sitting between his Eva's middle and index finger, cowering in fear.

"What the… two students from that private high school." said Misato as the two teens profiles appeared on one of the screens in the command room. "What are they even doing here?" Ritsuko asked as Shamshel closed in on Shinji.

The angel was now flying right above Shinji. It started making a crackling noise before it lashed out at Eva unit one in an attempt to rip it to shreds.

"**I don't think so Shamshel." **Shinji and the two boy heard a deep demonic voice call out as Shamshel's tentacles were cut clean off.

The angel let out a shrill sounding screech as it retreated away from Shinji. "How are you holding up Shinji?" Naruto asked as he floated lazily over Eva unit one. "Naruto, you're here." Shinji states happy that backup had finally arrived.

"Yeah sorry for being a little late, I had to synchronize with my new swords in order for them to work." Naruto explains to Shinji. Naruto then turns his attention to the two teens who were staring at him in awe.

"Hey Misato, I thought every civilian had evacuated to the shelters, what the hell are two teenagers doing here in the middle of an angel battle?" Naruto asked the woman, using a headset that Fuyutsuki had given him.

"That's what I would like to know however we don't have time for this, Shinji unit one doesn't have much time left, let those two in the cockpit and retreat." Misato commanded as Shinji opened his entry plug and aloud the two teens in.

"What the hell… there's water in here." One of the boys said as the other one started to complain about his camera getting all wet.

'What the fuck' Naruto thought as he turned his attention back to Shamshel.

Shamshel let loose a screech as his energy tentacles started to regenerate. "I had no choice you know, you did just try to kill one of my friends, how did you expect me to react?" Naruto asked the angel.

Shamshel let loose another screech and started making cracking noises at Naruto. Naruto grinned at the angel and spun his red swords around by a chain he had attached to them.

"Who or what I am is of little importance, all you need to know is that you are going to die." Naruto said as he activated the Rinnegan.

Naruto then used the Bunshin Ten'in so that is swords where floating beside him. Next, Naruto went through a chain of hand-signs before sucking into a large amount of air. 'Fire Style: Dragon Flame Jutsu.' Naruto produces a dragon head-shaped fireball from his mouth.

The dragon raced towards Shamshel, smacking right into its AT-Field. "HM, your AT-field is quite impressive, however can let's see how much it can really take." Naruto said as he started another chain of hand-signs.

"Wood style: Wood Dragon Jutsu." Naruto proclaimed as he created a gigantic wooden komodo dragon. The dragon roared at Shamshel as it ran at the angel.

Shamshel's deactivated it's AT-field and lash out at the dragon with its tentacles. The tentacles cut right through the dragons head. The head then reforms and the dragon rushes the angel, bites down on Shamshel's head once it got within range.

Shamshel screeches out in pain and began whipping the wood dragon with its tentacles, even though it was completely useless. Naruto grinned in amusement at the one-sided fight between his dragon and the angel.

"It hurts doesn't it, to know that you are completely helpless against something more powerful than yourself, now you understand how humanity felt when your kind took away their family, their friends and tried to wipe them off the face of this planet." Naruto said.

Naruto then grabs his new swords, then vanishes in a flash of yellow and appears right on top of Shamshel's head.

"Tell me something angel, have you ever experienced fear?" Naruto said as his swords started to charge up, turning from bright red to dark crimson. "Shamshel screeched in fear as it tried to escape the jaws of the wood dragon, which proved to be impossible.

What made it even worse was the fact that it's AT-Field wasn't working and that it was starting to feel really weak.

Naruto then jumps in the air and began spinning at extremely high speeds, while generating lightning on his twin blades. "Die, Lightning style: Dragon strike!" Naruto proclaimed as he shot ten huge lightning bolts vaporizing it's entire body except the core.

Shamshel let loose at soul piercing screech as it's body was turn to dust and it's core fell towards the ground. Naruto then caught the core and stabbed his swords into it, making sure that Shamshel would stay dead.

"The target has been eliminated, Naruto... Shinji return to base." Rei said as Naruto's dragon fall apart, leaving now that Shamshel was dead. Rei was standing in the command center beside Misato. She had watch the battle and while everyone was too shocked to say anything, she was not. Makoto said the other stared at Naruto, in awe of the former Hokage's power.

Naruto signed before flying back to NERV with the core in hand. "Naruto Namikaze… returning to base."

**END**

**There you have it guy's, chapter two is now complete. Naruto left everyone speechless once again. Just how powerful is he.**

**The Ritsuko I have chosen to us is the one from the rebuilds since she actually cares about Rei and the other pilots.**

**How will Shinji, Toji and Kensuke acted around him now that they've seem what he is capable of?**

**Find out in the next chapter of this story.**

**Make sure to Review rate and Subscribe as always and I will see you guys later.**

**Juubi no ookami signing out**


	3. Chapter 3

**Naruto Instrumentalities newest player chapter 3**

Ladies and gentlemen

The great god Juubi is here today, to bring you the third installment of Naruto Instrumentalities newest player.

I would have had this chapter out a lot sooner, however because I recently had to revise my entire schedule and it fucked up my flow.

Parings for this story

Naruto x Rei x Mari x Misato x Maya

Shinji x Asuka

**(Previously)**

"Tell me something angel, have you ever experienced fear?" Naruto said as his swords started to charge up, turning from bright red to dark crimson.

"Shamshel screeched in fear as it tried to escape the jaws of the wood dragon, which proved to be impossible.

What made it even worse was the fact that it's AT-Field wasn't working and that it was starting to feel really weak.

Naruto then stabbed both his MV swords into Shamshel's core, causing it to give one finally screech before it died a very painful death.

"Angel has been defeated." Makoto said as everyone stared at Naruto, in awe of the former Hokage's power.

"The target has been eliminated, Naruto, Shinji return to base." Rei said as his dragon fall apart, leaving Shamshel's corpse stand right where it died.

Rei was standing in the command center beside Misato. She had watch the battle and while everyone was too shocked to say anything, she was not.

Naruto signed before turning away from the bleeding angel core. "Naruto Namikaze… returning to base."

**(The moon)**

The moon, a natural satellite that orbits the earth. It is a large mass of space rock that merged together more than millions of years ago.

It was now a place that an organization known as Seele housed the Tabgha Base, the 7th branch of Nerv.

The base is situated on one edge of the giant red "blood stain" on the far side of the moon.

The base itself while huge, was largely unfinished. it is also sometimes referred to as the Provisional Excavation Base.

On the blood stain there lined up in a single row, there were nine coffins that if you followed would have led you to where they kept a being that closely resembled the second angel.

Inside the fifth coffin, a boy that look to be around the age of fifteen slept peacefully while somehow breathing in a place that had no oxygen.

The boy had grey hair that shines white while under the right light. His complexion is that of an extremely pale scrawny child and he was devoid of clothing.

Suddenly, the boy opened his eyes revealing emotionless red eyes and he had a serpentine-like smirk on his face.

This boy was none other than Nagisa Kaworu, the vessel of the first angel and the fifth child.

*Sigh* "I already know." Kaworu suddenly said as a monolith with the Seele logo and letters 01on it.

"If you have awakened me then that means that the child has appeared and we've entered the summation stage right." Kaworu said.

"Correct the prophecy of the Dead Sea scrolls has been passed into the book of law… the time with the covenant is close at hand.

"The third child again huh, you haven't changed." Kaworu said as he stood from the coffin and looked towards earth.

"I look forward to meeting you Shinji Ikari."

**(You can (not) reach out)**

"Man it's been three whole days." Toji groaned as he had laid his head down on the desk.

"What you mean since we were chewed out by Misato?" Kensuke asked as he was messing with his computer.

"No! I mean since we saw that Naruto person take out that angel, I mean he was only two years older than we are and he was able to kill that angel with relative ease." Toji said.

"Then there's the pilot Shinji Ikari, if it had not of been thanks to him then we could have been killed that day." Toji said.

"Are you worried about him?" Kensuke asked as he continued to type on his computer.

"No not particularly." Toji said denying what was obvious. "Okay class settle down." The teacher said as he entered the class.

"Today we have two new students." The teacher said causing the students to quiet down.

"You may come in now. The teacher said. The entire class was deadly silent as the door opened and the new students walked in.

The first to walk in was Rei Ayanami, followed by Naruto and Shinji. "I see that you were their escorts miss Ayanami." The teacher said as Rei went to sit in her seat.

Naruto then walked up to the chalkboard and wrote his name on it, while Shinji went to sit in one of the vacant seats.

After he was done, Naruto turned to address the class. "Good morning everyone my name is Naruto Uzumaki Namikaze, it's nice to meet you." Naruto said as he offered the class a foxy grin.

**"AH!"** every female student exclaimed in excitement. The girls' excited screams startled Shinji, Rei, and Naruto.

'Um… what did I say?' Naruto wondered as he sat in the seat next to Rei and behind Shinji.

(P.E.)

"Hey Naruto, Shinji can we have a word with you." Kensuke called out as he and Toji sat down next to them.

"Hey you're the two kids who got caught in the fight against the angel." Naruto said causing the Toji to start scratching the back of their heads in embarrassment.

"Yeah sorry about that, I guess we did kind of get in your way." Kensuke said. "No it's alright, no one got hurt so there's no need." Shinji said while waving his hands.

"However I had to see that awesome battle up close just once!" Kensuke proclaimed with stars in his eyes.

"That's all well and good but you two are lucky that you got off with just a tongue lashing from Misato, had that of been the commander there is no telling what the consequences would have been." Shinji informed the two teens.

"Yeah… I suppose that you are right." Toji said as he held his head down.

Suddenly, they heard the girls that had swimming class that day shout and splash around.

"They are something else aren't they?" Naruto said as they all turned towards were the girls where.

"EH! The boys are all over there gawking again!" One of the girls said as she hid behind another.

"Look Naruto-sama is also looking this way, is he a bad boy too?!" another girl asked as they all started squealing and giggling in happiness.

Naruto however had his eyes focused on Rei, who was sitting by herself and not participating with the rest of the class.

Naruto mind then drifted off to what happened to her during a sync test with unit 0 two days ago.

**(Flashback)**

"Begin activation." Gendo commanded as he adjusted his glasses. "Connecting main power to all circus." "

Power supply connected beginning system activation." The members of the Nerv's command center said as they started the activation process.

"Activation voltage is reaching critical level… 0.5, 0.2, rising." "Initiating activation system phase two."

"Pilot linkup initiated." "Start-up system phase two." The command center members said as Gendo, Ritsuko and Kozo all watched Unit 0's activation.

Suddenly as everything started looking to be a success, once the nerve links reached the borderline, Unit 0 started going berserk.

Unit 0 then broke out of it's restrains and started holding it's head as though it were in pain.

"Abort the experiment and cut the power supply!" Gendo commanded. "Yes Sir." A woman by the name of Maya Ibuki said as she pulled the emergency pug connecting the batteries cord to the Eva.

Unit 0 then switched to it's limited internal power and started moving toward Gendo who was watching from the command center.

The spirit of Unit 0 cried out in fury and punched the protective glass that separated the command center and the testing room.

Unit 0 kept on punching dents into the glass. Gendo who was standing right in front of the glass refused to move as Unit 0 continued it's rampage.

"It's gone berserk, get back commander!" Ritsuko said as Unit 0's auto eject system activated.

The entry plug then shot from the Eva and slammed into the walls with Rei still trapped inside.

"Dammit!" Gendo said as the plug continued to slam into the wall. "Hey! What the fuck is going on in here." Naruto exclaimed as he entered the command center.

"OH SHIT REI!" Naruto said as he felt Rei's life force signature coming from the entry plug. Naruto then phased through the room and ran over to Rei as Ritsuko ordered the activation of the Bakelite to hold Unit 0.

Unit 0 then begins banging it's head on the wall and roaring in pain until it finally shuts down.

Naruto who was now standing before the entry plug tried to open the super-heated hatch to save Rei.

"FUCK THIS SHIT IS HOT!" Naruto proclaimed as he pried the damn thing open. "Rei are you alright?!" Naruto asked as he entered the plug.

*pant* "Naruto… Why are you here?" Rei asked as she lifted her head to look at Naruto.

"I'm here to get you out you idiot why else would I be here?!" Naruto asked confusing the first child.

"Come on let's get you out of here so that I can heal your wounds okay." Naruto said as he lifted her up and carried her bridal-style out of the entry plug.

The members of the command center all watched in awe as Naruto exited the entry plug with Rei in his arms.

"Naruto is Rei alright?" Gendo asked as Naruto glared up at the man. "WHAT THE FUCK DO YOU THINK ASSHOLE?!" Naruto roared causing everyone with the exception of Rei to flinch.

"You… can you to escort Rei and me to the infirmary so that I can heal her wounds?" Naruto asked pointing towards Ritsuko as he phased back into the command room with Rei.

"Yes right this way." Ritsuko said as she led them to the medical ward.

**(End of Flashback)**

"Naruto… hey earth to Naruto." Kensuke said as Naruto came back to reality. "Huh… What?" Naruto asked as Toji and Kensuke had smug looks on their faces.

"So big shot who were you just staring so intensely at?" Toji asked as Naruto blinked a few times in confusion.

"Um… come again? Naruto asked not understanding what the boy was trying to imply.

"Oh he was just ogling Rei just now." Kensuke said as Shinji started chuckling, finding it somewhat funny.

"Aw come on…. We saw you looking." Kensuke said in a singsong manner. "Yeah at Rei's Tig Ol' Bitties." Toji said with a perverted look on his face.

"Rei's silky thighs, her calves, her… NAUGHTY BITS!" Toji and Kensuke proclaimed as they got into Naruto's face.

"Hey! Look you guys have got it all wrong." Naruto said while shaking his head. "Hey it's okay man after all, the girls all have such incredible bodies." Toji said.

'Yeah maybe to you guys, but to me the girls in this world can't compete with the kunoichi of my world in terms of sex appeal with the exception of Rei.' Naruto thought.

"Hey it's okay to admit that you find Rei attractive Naruto, we're all guys here." Shinji said.

"I think you're the last person to say that Shinji went you shy away every time Misato starts flirting with you while we're at home." Naruto said causing Shinji to blush.

Wait are you saying you guys are living under the same roof?!" Kensuke and Toji asked.

"Yeah we share a place with Misato and Rei." Naruto said as if it wasn't that big a deal.

"So that would mean that you two spend every waking moment with Rei and Misato?" Kensuke said as he and Toji started having daydreams of Naruto, Rei, Shinji and Misato doing some R-rated activities every night.

"Oh by the way." Shinji said bringing the two perverts out of their wild fantasies.

"I was just wondering why she's always alone." Shinji said.

"Come to think of it she hasn't had any friends since she was in junior high school." Toji said.

"I don't like the sound of that." Naruto said as they looked towards Rei. 'Although I had my suspicions.'

"There's just something about her that makes her hard to talk to, like she's in her own world." Kensuke said.

"She's just so gloomy which is a shame since she's so hot." Toji said as the coach called out to them.

As they were standing to leave Rei turned towards where they were and her and Naruto's eyes met for a brief second before the boys started running laps.

"I guess I'll just have to talk to her later on tonight." Naruto said.

**(Later that day at Nerv)**

Shinji and Rei were doing another synchronization test with the Eva's. Naruto had demanded that he be allowed to watch just in case he had to pull them out of the Eva.

After holding the entire Nerv HQ at gun point with the king of hell and threatening to murder Gendo by shoving a chakra rod the size of an Eva's arm up his ass they had reluctantly allowed him to stay and watch.

"Eva unit 1 is now entering the third stage cooling process, lower all systems to phase three and phase six."

"The harmonics and synchronization test results were good, all numerical conditions have been satisfied transfer the result immediately."

As Rei exited the entry plug Naruto entered the testing room and got Rei's attention.

"I see that it was a success this time around." Naruto said as Rei jumped down and moved closer to him.

"Yes I believe that somehow your presence was the reason why the Eva did not start going berserk." Rei said confusing Naruto.

"What makes you think that Rei-chan?" Naruto asked interested in Rei's little theory.

"While I was in the Eva, for some reason it I heard a voice say "he's watching" and unit 0 seemed to be focusing directly on you." Rei said as she look at Naruto with a curious expression on her face.

'Okay there's something very weird going on here I think I better look into this later on tonight after talking to Rei.' Naruto thought as Gendo walked up to them to congratulate Rei on her successful synchronization.

As Naruto watch Rei's interaction with Gendo, he narrowed his eyes once he realized that she had an emotionless smile on her face.

'Now that I think about it most of Rei's facial expression have been emotionless except for when she is staring at me in curiosity.' Naruto thought.

Shinji who was still inside Eva unit 1 also watched interaction between Rei and Gendo.

To him it looked a lot like Rei was genuinely happy while talking to his father and what shocked him ever more was the fact that Gendo was enjoying the chat as well.

**(One Hour later)**

"This is Nerv's head scientist and the chief of Project E Ritsuko Akagi." Misato introduced the woman to both Naruto and Shinji.

"It's a pleasure to Ritsuko-chan." Naruto said as he shook hands with the woman and offered her a smile.

"It's a pleasure to meet the enigma who has all these powers that can't be studied by running any of the medical test or the tests we use on angles." Ritsuko said.

"I must say that I'm very interested in you." Ritsuko said. "Oh is that so?" Naruto asked getting a not from Ritsuko.

Ever since that day Naruto had all but commanded her to take him to the infirmary and then kicked her out so he could heal Rei, Ritsuko couldn't wait to get answers out of him.

No that was a lie, she had been interested in him since the day he arrived.

Suddenly Ritsuko was swept off her feet and found that she was being held by Naruto bridal style. (She lost her shoes in the process)

"Well there are other ways that you could learn more about me, ways that are a lot better than simple test." Naruto said as he gazed into Ritsuko's eyes and offered her a sexy grin.

Ritsuko's cheeks turned bright red as she stared into the narrowed eyes of the Rikudō Sennin.

The way he held her in his strong arms without any difficulty and the look in his eyes as well as the foxy grin of his caused Ritsuko to become extremely hot and bothered.

Ritsuko then noticed that her hands were on Naruto's chest. Because of the face the Naruto was wearing a tight orange muscle shirt, Ritsuko could feel Naruto's muscular body.

She then started to imagine what it would feel like without his shirt. Shinji who was standing beside Misato had a huge blush on his face.

Misato on the other hand had a bewildered look on her face, not being able to process what was happening right before her eyes.

"I… um…. Well…" Ritsuko stuttered not knowing how to handle a situation like this.

"Here's an idea why don't you join us for dinner tonight." Naruto asked the woman.

"Um… sure if you'll have me." Ritsuko said unable to refuse this man that held her in his arms.

"Excellent then I'll see you then." Naruto said as he sat Ritsuko back on the floor and in her shoes.

"Misato I'm going grocery shopping, I'll see you guys a little later on." Naruto said before he disappeared in a bolt of lightning.

"What the hell was that all about?!" Misato asked as Ritsuko tried to beat down

**(Shinji and Rei)**

Shinji and Rei were getting ready to leave Nerv HQ when they had run into each other. Shinji had not been looking where he was going and had ended up running head first into Rei.

"Look Rei um… I'm sorry." Shinji said as he and Rei headed towards the exit together.

"About what?" Rei asked confused. "Well um… nothing I guess." Shinji said feeling uncomfortable.

"Hey Rei why do you pilot the Eva?" Shinji asked. "Aren't you scared Rei?" Shinji wanted to desperately know.

"Why do you ask?" Rei asked confused. "Well I heard that you were hurt in last week's experiment and an earlier one as well." Shinji said.

"Aren't you commander Ikari's son?" Rei asked. "Yes I am." Shinji said wondering where she was going with this.

"Don't you believe in your own father's work?" Rei asked hoping that would answer his question.

"No of course not!" Shinji proclaimed confusing Rei even more. "I see." Rei said as they took a train home.

After ten minutes of silent Rei asked him another question. "Do you trust us?" Rei asked referring to her, Misato and Naruto.

This question seemed to startle Shinji. He honestly didn't know how to respond to that.

'Do I trust Rei, Misato and Naruto, are they going to abandon me?' Shinji asked himself as he remembered Naruto saving him and offering him one of his special kunai.

**(Flashback day after Shamshel's death)**

"Here I want you guys to keep this with you at all times." Naruto said as he handed Shinji, Misato and Rei a tri-pronged kunai.

"What is this for?" Rei asked as she stared at the kunai in her hand in wonder. "I think this is a little too dangerous to just be carrying around Naruto." Misato said.

That kunai is a special tool that will summon me anytime you guys are in trouble." Naruto said.

"To be honest, I'm scared of Naruto and I can't allow myself to get close to Misato." Shinji said feeling sad that he couldn't trust the people who were trying to get closer to him.

"I mean Naruto has these powers that can't be explained and I even seen that

Suddenly, Rei slapped Shinji across the face with all her strength, sending the boy to the floor.

Shinji lightly touched his right cheek before look up at Rei with a shocked expression on his face.

As for Rei, she glared down at Shinji. How could he say something like that after Naruto had risked his like to save the boy?

Naruto had even given them a way to transport him to their location and even promised to protect them.

"_Remember this, no matter where you are, no matter what kind of trouble you get yourself into, just throw this and I will be there in a flash to protect you." Naruto said with a foxy grin spread across his face._

_I give you my word as the Rikudō and the sixth Hokage, but most importantly I give you my word has your friend._

As the train finally came to a stop, Rei got off of it and walked the rest of the way home.

Shinji who by now had a depressed look on his face stayed behind as the door to the train closed and left. The station.

As Rei watch home, she pulled out her tri-pronged kunai.

The words that Naruto had said the day he pulled her out of Unit 0 echoed through her head.

As Rei stared at the first gift that she had ever received, an emotional change causes certain muscles in her face to tense, producing an expression.

**End**

**Well there you have it. the third chapter is finally complete. not a lot of action in this chapter.**

**Shinji is running away. well stop the fucking presses. sarcasm**

**Next chapter will have more action and plenty of Naruto x Rei moments to go around.**

**RATE AND REVIEW and I'll see you guys during the next installment.**

**This is Juubi **

**The progenitor of life signing out**


	4. Chapter 4

**Naruto Instrumentalities newest player Chapter 4**

Ladies and gentlemen

Juubi the king of Biju is here today, to bring you the 4th installment of this Naruto x Evangelion crossover.

One last thing make sure that after you read this you remember one thing, Naruto is a Shinobi.

Parings for the story

Naruto x Rei x Mari x Misato x Maya

Shinji x Asuka

**(Previously)**

Shinji who by now had a depressed look on his face stayed behind as the door to the train closed and left. The station.

As Rei watch home, she pulled out her tri-pronged kunai.

The words that Naruto had said the day he pulled her out of Unit 0 echoed through her head.

As Rei stared at the first gift that she had ever received, an emotional change causes certain muscles in the face to tense, producing an expression.

**Hedgehog's Dilemma and the Souls within**

"Hey where is the food, I'm starving over here!" Misato exclaimed as she and Ritsuko entered the house.

*Groan* "Oh great and she just had to come home half-drunk didn't she." Naruto complained as he continued to cook.

Naruto was cooking some Oden, Udon Tonkatsu, Hayashi Rice, Hiyayakko, and Ramen.

During Naruto's travels with the toad sage Jiraiya, Naruto had created storage's that he used to store large quantities of food.

The Oden comprised of various fish cakes, daikon, boiled eggs konyaku and Kombu seaweed that was slow simmered in a soy sauce based soup.

Udon are noodles served with tempura and mountain vegetables.

The Tonkatsu are deep fried pork cutlets served with curry rice. Hayashi rice is Japanese style hashed beef stew, thinly sliced beef and onions in demi-glace sauce served over cooked rice.

The Hiyayakko is fresh chilled tofu garnished with grated ginger, Katsuobushi (shaved bonito flakes), green onions and seasoned soy sauce.

Finally the Ramen was noodles prepare fish broth flavored with miso, sliced pork and a boiled egg.

Rei was sitting at the table in pajamas.

"Sorry about this Naruto, I tried to stop her, but by now you know how she is when it comes to sake and food." Ritsuko said causing Naruto to shake his head.

"Just make sure she gets to the bathroom if she starts feeling sick, would ya." Naruto said as he continued to cook.

Misato who was leaning on Ritsuko's shoulder with her head down, raised her head to watch Naruto cook in the kitchen with an apron on.

She then stood up straight and headed to her room. Ritsuko then sat at the table and watched Naruto as he cooked.

She studied him from her seat.

As she watched, she noticed that she wasn't reacting to him like she did earlier that day.

This actually surprised her as she had been extremely aroused when he held her, however now she just seemed to regard him casually.

'Why was I so aroused when he held me earlier, why is that?' Ritsuko wondered.

Naruto grinned as he felt Ritsuko's calculating graze.

Being able to sense human emotion, Naruto could tell that she was extremely confused about her feelings.

"Hey Naruto where is Shinji?" Misato asked as she came out of her room. Misato had changed out of her work clothes and now wore a tank-top and short-shorts.

"He didn't get off the bus when we took it earlier." Rei said as Naruto gave her an amused look that he knew what had happened.

"Ah yeah about that, he met Kensuke who was camping out in the woods." Naruto informed them while Rei gave Naruto a bored look.

Misato sighed and sat at the table. "That Shinji… I guess its best that I have a talk with him once he comes back." Misato said.

"I think you should leave that to me Misato, its best that he speak to someone who is around his age." Naruto said as he started putting the food onto plates.

*Sigh* "Yeah I suppose your right, he just so much more naive than I expected him to be." Misato said in defeat.

"What's this, complaining already, you wanted the one who insisted on living here with Shinji, Naruto, and Rei?" Ritsuko said with a smug look on her face.

"Oh shut up." Misato said as Naruto placed their food on the table.

"She is right you know." Naruto said getting their attention. Naruto then created a shadow clone and handed it two plates of food.

"Have you ever heard of the hedgehog's dilemma?" Naruto asked as his clone vanished in a swirl of black flames.

"Hedgehog's dilemma? You mean those little spiky critters?" Misato asked.

"You see with hedgehogs, even if they want to get close to each other for warmth the closer they get the more they risk hurting each other with the quills on their bodies." Naruto explained.

"Basically it's no different from people, Shinji is worried about what will happen if he lets someone get too close, he's fear of that pain causes him to pull away completely." Naruto finished explaining.

"Well he'll figure it out someday, that part of growing up is to allow herself to get hurt sometimes." Misato said as Naruto sat down at the table with them to eat.

"To keep letting people in until you finally find that safe distance where you can finally find that safe distance where you could be close without hurting each other to much." Misato said.

"I hope your right." Ritsuko said. Rei just sat in her chair at the table listening to their conversation.

Listening to Naruto explain what Shinji was suffering from, a thought suddenly entered her head.

'Did you have to go through a similar situation Naruto?' She wondered. Noticing her look, Naruto gave her a smile before patting the top of her head.

"Well enough about that, why don't we all enjoy our dinner." Naruto suggested, which caused Rei, Misato and Ritsuko to grab their chopsticks.

"Ok it's time to eat!" Misato proclaimed as she and Ritsuko took a bite of their Oden and Udon respectively.

*O_O*

*AH!* Suddenly, Misato and Ritsuko both dropped their chopsticks into the food. They then turned to look at Naruto in shock.

"What?!" Naruto asked wondering why they were giving him that look.

"Naruto… just how did you make this?!" Ritsuko asked as she picked up her chopsticks.

"Just how did you make it so flavorful?" Misato asked as she took another bite.

"It's good." Rei said as she tried some of her Hiyayakko.

"Well I'm glad that you like it, it actually took me and my three fiancées a long time to come up with this recipe." Naruto said with a happy grin on his face.

"Oh well I have to say….

*Cue Record Scratch*

"Wait what did you just say?" Misato asked as she and Ritsuko look towards Naruto.

"Oh I guess I haven't told you yet." Naruto said before he pulled out a picture of him and his three deceased lovers.

"Here is a picture of us." Naruto said as he should them the picture.

"The girl with short black hair, holding a pig and my third fiancée Shizune." Naruto said.

"The girl in the royal kimono is the princess of a nation in the land of snow, Koyuki Kazehana my third fiancée.

Finally the girl in the middle is my first fiancée and the princess of one of the most powerful clans in my world, her name is Hinata Hyuuga.

Misato and Ritsuko looked from the picture to Naruto and back with a bewildered look on their face.

Suddenly, their look turned somber look. "What's that look for?" Naruto asked with a calming smile on his face.

"You seem a lot happier in this picture." Misato said causing Naruto to smile.

"This was taken right before the war," Naruto said as he looked towards Rei.

Rei looked at the picture in curiosity and then to Naruto with a look that actually surprised Naruto.

Naruto then placed his hand on Rei's head and offered her a smile. "I'd like to tell you the story one day however for now let's just enjoy our dinner."

**(Shinji and Kensuke campsite)**

"Oh did you know that Toji had a younger sister?" Kensuke asked Shinji who was sitting across from him with a somber look on his face.

"Toji has been complaining lately about how his little sister begging him to introduce her to the pilot of the Eva." Kensuke said.

"It must be hard having to deal with a second grader when they beg for things." Kensuke said. Shinji did reply and instead chose to stare into the campfire.

'Hm there seems to be something bothering him.' Kensuke notices as he continues to try to get Shinji to speak.

"You know I really enjoy it out here at night, because those noisy Cicadas don't chirp."

"It was pretty quiet when I was a kid, but there are tons of them now." Kensuke said.

"Misato said that the ecosystem is returning to its original state." Shinji said.

"Oh Misato said that huh, you know I really envy you and Naruto Shinji." Kensuke said.

"I mean you two live with two beautiful women and you get to pilot the evangelion."

"Ah man I wish I could get inside that lovely cockpit just once." Kensuke said as he started making battle sounds.

"You really shouldn't you know." Naruto said as he made his way to their campsite.

"Oh hey Naruto what brings you here?" Kensuke asks.

I had dinner cooked for you guys since you told me you were camping tonight." Naruto said as he handed both Kensuke and Shinji them the Tonkatsu and Hayashi rice respectively

"Naruto's right you know, your mother would be worried." Shinji said confusing Kensuke.

"Huh my mother? Oh don't worry about my mother, as a matter of fact I don't have one of those." Kensuke said shocking Shinji although Naruto already knew this.

"I'm no different from you in that since. Kensuke said. "What about you Naruto?" Kensuke asked.

"Well I suppose I can tell you if you promise that you won't tell Misato and Rei or anyone else." Naruto said while giving Kensuke and Shinji a look.

Kensuke then stood up and placed his hand over his heart, doing a very good impression of the solute human's once did when they recited the pledge of allegiance "I promise on my live Naruto!"

"Reading the boy's emotions, Naruto knew that he could trust the boy. Looking over to Shinji, Naruto was quite surprise when he saw the down look on Shinji's face.

"I don't think that I deserve to know Naruto, not after what happen today." Shinji said as the somber look returned to his face.

"You mean the conversation you had with Rei earlier today right." Naruto said causing Shinji to flinch and look away from Naruto.

Kensuke stared looked towards both of them, not knowing what was going on.

"I had a clone of myself there when you two were talking on the bus, Rei did not tell me." Naruto informed him.

"You don't have to worry about me being angry Shinji, it's perfectly normal for humans to fear what they don't understand and while you are scared of me, you do regret it." Naruto explained.

Shinji looked up towards Naruto in surprise. He had expected Naruto to be extremely pissed about it, however he was a lot more understanding about it.

"But Misato and Rei seemed to not be afraid of you, and you make Miss Ritsuko fall for you." Shinji said.

"Wait a second, what's this about Naruto having Ritsuko fall for him?" Kensuke asked with a bewildered look on his face.

'Oh yeah I forgot that I had used my pheromones on her while Shinji was watching.' Naruto thought.

"Are you referring to Ritsuko Akagi, Nerv's top leading scientist?" Kensuke asks causing Shinji and Naruto to give him weird looks.

"Yeah she is who we are talking about." Shinji said.

Suddenly, Kensuke turned towards Naruto and bowed his head to the sage of six paths.

"Please… teach me the art of wooing women Naruto-sensei!" Kensuke said causing Naruto to gain a droplet of sweat on the back of his head.

"First off, raise your head Kensuke, as this is starting to get really awkward." Naruto said as the boy sat up straight.

"Second, my relationship with Misato works so well, because we have mutual respect for each other and have a few things in common." Naruto said.

With Ritsuko I noticed that she seemed to be "extremely frustrated" and since I was feeling that way as well, I thought it would be beneficial for the both of us if we came to an agreement." Naruto said.

While this was an obvious lie, Naruto once had to use his pheromones on women during some of his missions.

Shinji and Kensuke both turned bright red at as they pictured Naruto and Ritsuko in various sexual position that you can find in most karma sutra novels.

"As for Rei… well she seems to be trying to figure me out and I find her extremely cute, so do I really need a reason?" Naruto asked them.

"Good point." Shinji and Kensuke said at the same time.

"Good and now I believe it's time for me to go." Naruto said as he stood up.

"Oh and Shinji, you shouldn't feel down about your fear of me, over time it will fade and you will come to see me as someone you can trust with your life." Naruto said before disappearing into a poof of smoke.

**(Back with the others)**

"I gets I'll see you tomorrow at the base Misato" Ritsuko said as she put on her shoes and got ready to walk out the front door.

"You could have stay you know." Misato said causing Naruto to give her a weird look.

"Sorry but I have something to look at before I go to bed tonight." Ritsuko said waving Misato off.

"Besides I'm walking her home so it's not as if something bad is going to happen to her." Naruto said causing Misato to look at him in suspicion.

"Oh I wonder about, after all you did try to put the moves on her earlier today, Should I can't let you have your way with her." Misato accused.

"Hey I wasn't going to take advantage of her if that's what you are thinking." Naruto said.

"It's quite alright I wouldn't have mind all that much if he did." Ritsuko said causing Misato who was drinking beer to spew it from her mouth much to Naruto and Ritsuko's amusement.

"Ritsuko what the hell!" Misato exclaimed casing Naruto to laugh his ass off.

"What you said that you weren't planning on making a pass at him or Shinji, so why can't I?" Ritsuko asked causing Misato's face to go red in embarrassment.

"Oh really well I have to say that I'm a little disappointed." Naruto said with a pout on his face with was so forced that even Rei noticed it.

"Oh well, shall we go then Naruto?" Ritsuko asked. "Yes let's be on our way Ritsuko." Naruto said as they both walked out the front door, leaving a clearly flustered Misato.

"You jerks!" Misato exclaimed before walking back to the kitchen with Rei following behind her.

After sitting in at the table Misato began to down another can of beer to drown her frustrations.

Rei watched her for about a minute before she decided to ask the older women a question. "Misato what does having you way with someone and making a pass mean?"

***Cue Spit take***

*Coughing* "Why would you ask that?!" Misato asked the girl who had a curious look on her face.

"Also I would like to know what Naruto did that made you question Naruto's motives." Rei asked not being able to understand what they were talking about

'Oh why me.' Misato thought with a groan.

**(Naruto and Ritsuko)**

"So what's this talk about making a pass on me or Shinji?" Naruto asked Ritsuko. Because it was dark out Naruto was able to fly over the rooftops without any human noticing.

"Oh it was just some girl talk after you and the others had left." Ritsuko said as she held onto Naruto's back.

"I see, so what do you say my chances are with her." Naruto asked deciding to keep the conversation going.

"Oh so you like her and here I was expecting you to go after Rei, since you two have been almost inseparable likely." Ritsuko said.

"I'm not really going after either of them, it was just a passing thought." Naruto said.

Ritsuko frowned as she noticed that she couldn't tell if Naruto was telling the truth or lying.

"I see, well I think that you have an sixty percent chance with Misato, however I'd say only a thirty percent at best." Ritsuko said.

Naruto grinned once Ritsuko said that. "I like those odds." Naruto said just low enough so that Ritsuko did not hear him.

Upon reacting Ritsuko's house, she got off Naruto's back as walked up to the door.

"Oh and before you go, could you give these too both Rei and Shinji when you see them?" Ritsuko asked as she handed Naruto some new ID cards.

"Oh these are the new cards." Naruto states. As he looked at the one with his name on it.

"That's right so you can throw away the old ones." Ritsuko said before opening her door and walking inside the house.

Naruto watched as she closed the door and turned to walk away. "She thought that I would use that woman for my desires." Naruto said with a look of disgust on his face.

"I'd never allow myself to be in the bed of a woman who is that desperate to sleep with that man and has no self-respect." Naruto said having looked into the woman's memories.

'Still that was a lot easier than I thought, now that I have her card, I can get into Nerv without a problem.' Naruto thought as his eyes became the Rinnegan and a dark grin spread across his face.

Naruto then vanished into a swirl of wind.

**(Ritsuko)**

"Well I guess I should take a quick bath, before I go over that paperwork." Ritsuko said as she headed towards her bathroom.

After taking a shower she entered her living room only to notice that the lights were out and one of her candles was lit.

'Wait I didn't light that candle.'

"I see that you are doing well Ritsuko Akagi." Gendo said as he made his presence known.

"Oh Gendo I didn't notice you come in, what can I do for you." Ritsuko said wondering if he was there to talk business.

"I am here as per our deal Ritsuko." Gendo said as he removed his tie and started to unbutton his shirt.

Ritsuko blushed and unconsciously licked her lips. "Okay but allow me to service you." Ritsuko purred as she walked over to him while slowly swaying her hips back and forth.

She then took off his belt and pulled pants and got down on her knees.

Ritsuko then pulled his underwear down and grabbed his dick, which right now was standing at attention. (I'm gonna be sick)

Ritsuko then licks the tip before taking him into her mouth. She then began to bob her head back and forth while slurping on Gendo, causing the man to groan.

*Groan* "As usual you are very skilled at this technique." Gendo said. Ritsuko let out a moan which caused Gendo to cum in her mouth.

'It's a lot more than usual, I wonder why' Ritsuko thought as she swallowed his cum.

"I believe that it's time to start the next phase." Gendo said causing Ritsuko to look up at him only to come face to face with a gun.

"Thank you for your cooperation, you are now being relieved from duty." Gendo said as he shot a wide-eyed Ritsuko right in the head twice.

"Without even so much as a scream, Ritsuko's body fell limply to the floor. A pool of blood flowing from under her body.

"So it's finally done." a distinct female voice asked from the shadow of the room.

"Yes and with this your mission can begin." Gendo said causing the woman to giggle.

"But before then, how's about we finished what she couldn't." the woman said seductively as more candles lit up the room.

**(Naruto)**

Naruto stood before the Eva's with a calculating look on his face. 'Alright I guess it's time to finally meet the three souls that have emerged with the Eva's.'

Naruto then held up a hand-sign and summoned the king of hell. The demon rose up from the depths of hell in all his glory.

It then placed its hands on both Eva unit zero and Eva unit 1. Naruto then sat on its head and got into the lotus position while also activating the Rinnegan.

"Sage Art's: Soul Resonance!" Naruto proclaimed as the room was engulfed in darkness.

Inside the darkness Naruto came face to face with two individuals.

The first was a beautiful young woman who looked like an older version of Rei except that she had a different hair color and she had this kind and gentle look in her eyes that caused Naruto to blush.

The second person was a carbon copy of Rei with the only difference being that she had the appearance of an eight year old.

This was known other than Yui Ikari and the first clone of Yui Ikari who was once killed by Naoko Akagi.

END

Holy shit Ritsuko brains got splattered all over the floor, by Gendo and who was that woman with him.

To all those who thought that Ritsuko was a part of the harem well sorry but this isn't some normal harem and Naruto is a ninja who will use everything in his arsenal of skills to get what he wants.

And what he wanted was Ritsuko's knowledge.

Make sure to leave a "REVIEW" for this story and I'll see you all next time

**This is Juubi the god of Biju signing out**


	5. Chapter 5

**Naruto Instrumentalities Newest Player Chapter 5**

Here is the 5th installment of this story.

Paring for the story

Naruto x Rei x Mari x Misato x Maya

Shinji x Asuka

**(Previously)**

"**Sage Art's: Soul Resonance!" Naruto proclaimed as the room was engulfed in darkness.**

**Inside the darkness Naruto came face to face with two individuals.**

**The first was a beautiful young woman who looked like an older version of Rei except that she had a different hair color and she had this kind and gentle look in her eyes that caused Naruto to blush.**

**The second person was a carbon copy of Rei with the only difference being that she had the appearance of an eight year old.**

**This was known other than Yui Ikari and the first clone of Yui Ikari who was once killed by Naoko Akagi.**

**You can (not) protect**

Yui Ikari and the first Rei Ayanami clone both stared at the endless void in wonder.

Ever since they had become trapped within the evangelion, they had been experiencing events in a sort of out-of-body experience.

"Now however it felt as if they had finally awoken and were experiencing what it meant to be in control of their body for the first time in years.

"So how does it feel to finally be back with your bodies once again after so long, Ikari-san?" Naruto said gaining the beautiful young mother's attention.

Yui stared at Naruto in confusion, wondering who this boy standing before her was and then it suddenly, hit her as a memory of the boy devouring an angel's S2 Engine entered her mind.

"You are that child who killed two angels on his own and without the use an Eva." Yui said as she gained that look in her eyes that most scientist seem to have when they find something that they wish to study.

"So you were conscious during that as well, though I would appreciate it if you didn't stare at me like I'm some kind of research subject." Naruto said causing the woman to look away in embarrassment.

Suddenly, Naruto felt Rei pulling on his hand and he looked down giving all of his attention to the little girl.

"Oh I'm sorry for ignoring you Rei." Naruto said as he rubbed the little girls head.

"Naruto-san why are we floating in a void, is this the border that leads to the afterlife?" Rei asked wondering if she was going to be eaten by that demon that Naruto had used to bring them here.

"What makes you ask that? Naruto asked the girl in confusion while making a note of the fact that the girl looked like she was expecting to be killed once again.

"I share memories with the other Rei clone and you once said that it devours souls." Rei said causing Naruto to pat the girl on the head.

"You have nothing to worry about little one, I only came here to meet the two of you." Naruto reassured the little girl who tilted her head in confusion.

"Who is that child Naruto-san?" Yui asked as she had never met the little girl that acted as the soul for unit-00.

"Ah that's right I suppose that I should introduce the two of you." Naruto said confusing Yui.

Naruto then picked up the little girl and turned to face Yui. "This little girl was created from the 'salvaged remains' of Yui Ikari who was absorbed into unit-01, so in a way she is actually your clone Yui." Naruto informed the woman who gasped in surprised.

"My clone?" Yui asked with a flabbergasted look on her face. Who would make a clone of her?

"It was Gendo Ikari who created Rei when he tried to bring you back." Naruto informed her.

Yui looked at the little girl in wonder for a few seconds before she offered her clone a motherly smile.

Rei stared at her in confusion, while Naruto was in awe of the radiance of Yui's smile.

"I glad to finally meet you Rei-chan, I hope that you can forgive me for my reaction, I was just surprised is all." Yui said as Rei gave to woman a hesitant nod, while holding on to Naruto.

Suddenly, the knowledge that the girl was here with them, suddenly dawned on the mother and she turned to asked Naruto.

"Why is she here in the place with us?" Yui asked causing Naruto to sigh.

Unfortunately she was murdered and had her soul infused within unit-00." Naruto said his red flashed red for just a slit second.

Yui placed her hand over her mouth as she stared at the little girl in Naruto's hands.

The fact that this child was created from her remains, while shocking was not that big of a deal, and even nothing the fact that Gendo had created the little girl was only a minor problem.

However the knowledge that this little girl was murdered was horrifying. Yui who by now was shaking like a leaf in the wind, reached out towards the little girl.

"Who… who did this?" Yui asked Naruto who had his eyes closed, trying to calm himself down so as to not shatter his connection.

"She was murdered to the age of four by a woman named Naoko Akagi, who strangled her to death." Naruto said causing Yui to gasp in surprise.

"It can't be, that has to be a lie!" Yui proclaimed causing Rei to stare at her with a haunting expression on her face.

"It was a memory that her daughter Ritsuko had seen with her own eyes, I on the other hand read Ritsuko Akagi's mind." Naruto informed the woman, who by now was in tears.

"It was this memory and another memory of Ritsuko herself attempting to strangle my Rei, who is the second clone that Gendo created after he infused her with unit-00." Naruto said.

"But… why would Naoko do something like that, she's not the kind of person who would kill a child, I mean for Lilith's sake she has a daughter of her own." Yui said as she sank to the nonexistent floor.

"She did that because I told her the truth about Gendo Ikari using her while they were having an affair after your death." Rei informed Yui who looked up at them.

"It's the truth, and now he is using her daughter, who had known what was going on between them, but decided that she wanted him as well." Naruto said.

By now Yui had felt as if her entire world had just been shattered… no obliterated right before her very eyes.

"With red eyes Yui stared into Naruto's own blood red demonic ones and she asked.

"What about my son, where is my Shin-chan?" Yui asked as she stared into Naruto's eyes, not even noticing the fact that they look like the eyes of the devil himself.

"After you quote on quote 'died', Gendo had abandoned the boy and sent him to live with your relatives shortly after he had witness you disappearing within unit-01 and after they had died he lived with his sensei." Naruto informed her.

The man only seen Shinji as a liability and now only sees the boy as a weapon to fight the angels and nothing more.

"As a result he is plagued by self-doubt and feelings of worthlessness, he is apathetic, depressive."

He is shy and introverted around others, although he has been able to at least make two friends other than myself.

He also has an audacious and cynical thought process when dealing with others." Naruto informed her as he had heard Shinji call Rei a cold-hearted bitch in his mind before the boy had regretted it.

"I see, it seems that I was wrong about that man all along." Yui said as she stood up and wiped the tears from her eyes.

"Thank you Naruto-san, for telling me this." Yui said as Naruto let Rei down. Naruto then placed his hands on Yui's shoulders, causing her to look up into Naruto's now azure blue ones.

"No need to thank me, I have adopted him as my little brother and I won't allow anything like that to happen ever again, you have my word." Naruto said.

"That means that if I have to I will have to dispose of Gendo and destroy Nerv, if it means protecting him and the others." Naruto said.

After hearing this Yui gave Naruto a heartwarming smile that caused Naruto to blush again.

'Well I can see why even someone like Gendo could fall for her.' Naruto thought as he leaned forward.

Rei watched the two as Yui closed her eyes and parted her lips, anticipating the.

Suddenly, Naruto felt the presence of another being appear at the entrance of headquarters.

Naruto let go of Yui and brought up an image of the person.

"Naruto what's wrong?" Yui asked wondering what got the young man's attention. Naruto glared at the image of the person who wore a hood to conceal his face.

"I will have to cut our meeting short for the night my princesses, there is a rodent infestation." Naruto said as he got ready to sever the connection.

"Wait before you go Naruto-kun, promise me that you will also protect the girl who is still alive and make her happy." Yui pleaded with the boy who offered the woman a smile.

"I promise Yui."

**At the entrance**

A person wearing a hood walked up to the entrance to Nerv headquarters at a leisurely pace, when a strong wind blew through the area.

"It's kind of late for a stroll ain't it." Naruto said as he appeared right behind the person.

"Hm it would appear that there was someone other than I who was sneaking around the lilin's base of operations." The person said.

"Lilin you say…? I see so you are not human after all." Naruto said finding this situation interesting.

"So I suppose that you are here to be a nuisance." The person casually states causing Naruto to shrug his shoulders.

"That depends on what you are after." Naruto said as he activated the Rinnegan.

"The complete eradication of the lilin race, though I suppose that I must first do battle with you, child descendant of the tree of darkness." The person said as angel wings grew from his back.

'He knows what I am I see, this has gotten even more intriguing.' Naruto thought

**He Who Howls and Rages**

"**Let's go." Naruto commanded as the two titanic beings vanished in a burst of speed and began to clash through the dark skies.**

Faster than the naked eye and powerful enough to cause rippled that could even be felt by those on the ground.

Lightning and fire zipped through the skies as they continued to ram into each other.

Naruto blitzed towards the angel with his twin swords. The angel generated an AT-Field strong enough to withstand Naruto's blades.

The angel grinned as he sent thunder and lightning that his AT-field generated through Naruto blades and into his body.

"**AHH!" Naruto roared as the thunder and lightning coursed through his veins.**

The grin that was on the angels face however turned into a frown as Naruto jumped away from him and seemed to have shook off the effects after a few seconds.

'That output of electric waltz was enough to destroy a hundred lilins in seconds, and yet he doesn't even have a scratch on him, he truly is a devil.' Ramiel thought.

"**Hm so you really are an angel." Naruto notices as he descends towards the ground.**

"This lilin body is amazing is it not, to thing that they can be very useful as vessels for us, it is true magnificent!" The angel proclaims as he removes his hood, revealing the face of a teenage boy with white hair and platinum gray eyes.

"**Disgusting, you have defiled the purity of the lilin with your tainted soul." Naruto said causing the man to laugh.**

"This coming from a child of the darkness, HA! Don't make me laugh!" The angel said as he generated a building size ball of electromagnetic energy.

"I am the 6th angel Ramiel, and I shall be your executioner." The angel of thunder proclaimed.

"That enough Ramiel, you've overstepped your boundaries." Another angel said as he appeared right behind him and shattered the bolt of lightning.

"Tabris you dare to get in my way, you damn lilin lover!" Ramiel growled at his brother who glared down on him as if he were a lower being.

"You were only supposed to infiltrate Nerv without being detected, and if you should be discovered you are to retreat." Tabris said causing Ramiel snort in disgust.

"Enough talk fools!" Naruto proclaimed getting the two angels attention. "I could care less about the reason why you've come here." Naruto said as he summoned his wood dragon.

"Just know that I will kill each and every last one of you that wish to eradicate the lilin." Naruto casually proclaims causing Ramiel to growl in anger.

"Let's go Ramiel we are done here." Tabris commands as he disappears.

"Insolent beast, I will enjoy sending you to hell where your kind belongs. Ramiel proclaimed before he vanished as well.

'So it has truly begun, the battle between the 18th angel lilin and those descendants of Adam." Naruto thought as he looks towards the moon.'

"It appears that our meeting will happen ahead of schedule… Lilith."

Deep within the subterranean cavity of Nerv known as the Geo Front, Lilith raised her head as she felt the presence of a life form equal to herself and Adam.

'The Shinju will appear within the realm and it will target all those closest to you in order to draw you out … what will you do child of darkness?" The second angel subconsciously asked the fallen child.'

As she unconsciously looked towards the surface, the pool of LCL started to wave and shift as a spear that was identical to the one that pierced her chest and pinned her to a cross shape structure, rose out from the bottom of the pool and vanished.

**(Early the next morning)**

Naruto returned back to the house he shared with the others. "I'm home!" Naruto called out, even though he knew he wouldn't get an answer.

After taking off his shoes and cloak, Naruto headed towards his room deciding that he would sleep for the rest of the day.

As he passed by Misato's room, he could hear both Misato and pen-pen snoring as they slept in drunken bliss.

'They are both going to wake up hung over.' Naruto thought with an amused grin on his face.

As he entered his room Naruto was startled with he came face to face with a wet and naked Rei, standing beside his bed.

'Oh you have got to be shitting me.' Naruto thought as he admired the beautiful young woman, whose skin seemed to sparkle as droplets of water rolled down her body.

Rei stared at Naruto in confusion as she noticed the look on his face. She had no idea what that look meant, however for some strange reason she found that the look didn't bother her like it should have.

In fact, she seemed to feel oddly satisfied that he was looking at her though she didn't know why.

"What?" Rei asked while tilting her head to the side. Naruto blushed and turned away from the alluring beauty that was ass naked right before him.

"You should really learn how to lock a door when you are using the shower Rei-chan." Naruto said as he places he hand on his face.

"Why? Rei asked as she started to feel slightly amused by Naruto's reaction for some reason.

"Because what if someone other than I walked in on you changing, like Shinji for instance." Naruto said while Rei got dress.

Rei didn't say anything as Naruto took a peak at her as she was bending over to put on her panties.

"Beside what would you do if I was the kind of person that would take advantage of this situation?" Naruto asked as he started scratching his whisker marks.

"What?" Rei curiously asked Naruto.

"Never mind I'm going to sleep." Naruto declared as he talked over to his bed and lays down on it.

Having finished getting dressed, Rei starts to head for the door, but stops and turns to see that Naruto was laying on top of the bed on his back.

Her focus went from his blonde hair to his slightly pointed ears. She then took notice of the whisker marks on his cheeks.

"She then moved quietly over towards Naruto and reaches towards Naruto's face. Rei then runs her index finger along his right cheek.

Naruto response to this is to purr in contempt. Rei moved her hand away from Naruto when she got this response from him.

She had been expecting him to say something about her touching him in that nonchalance manner like he normally does, however much to her confusion he was already asleep.

Taking advantage of the situation and surprising herself, she continued to massage Naruto's cheeks.

Rei's own face seemed to gain some red tint as she studied Naruto's reactions, finding them to be very appealing to her and she continued this for the rest of the day.

**(Two days later)**

Both Kensuke and Shinji were awakened by the sound of footsteps heading in their direction.

Kensuke turned towards Shinji and gave him a look before he sprang to his feet, shotgun in hand ready to take out the intruders.

Upon seeing that it was Nerv personnel though he stared at them in confusion as to why they were hear until he remembered that Shinji was right there next to him.

As Shinji walked out of the tent, the man that was closest to the tent the addressed the.

"You're Shinji Ikari aren't you?" The man dressed in black asked.

"Yes what is it that you want?" Shinji asked the man.

"We're from Nerv security intelligence, under security clause article 8, we are taking you to Nerv headquarters.

Shinji stared at the men for a whole minute with a blank expression on his face before he strengthened his resolve.

"Yes it's time to head back, they are all waiting for me." Shinji said before turning to Kensuke.

"Thanks for the hospitality Kensuke, I'll be seeing you at school." Shinji said before leaving with the men.

**(At school later that day)**

"So all you did was stand there?!" Toji asked Kensuke as they talked in class during their lunch break.

"That's easy for you to say, but they were Nerv intelligence… professionals." Kensuke informed Toji who was pissed that he just let Nerv take Shinji away without a fight.

"So what about it, geez don't you have any balls at all?!" Toji asked loud enough for the girls in the room to hear.

They then started calling him names like creep, ape and pervert, while giggling to each other.

"Only an idiot fights when he knows he can't win, balls have nothing to do with it." Kensuke said not at all bothered by Toji's little outburst.

**(Nerv)**

Shinji had been confined to a dark room within Nerv as soon as he got back and had yet to meet up with Naruto or Rei.

He wanted to find Rei and try to rekindle with her and he wanted to find Naruto and apologize to the demon descendant for his irrational fear of him.

This however was not meant to be for the time being as he sat in the room.

Suddenly, the door to the room opened and in walked Misato looking unsure of herself.

She had at first been sort of hesitant in coming to meet with him and had begged Naruto to come see him, even though she wanted to see Shinji and try to comfort him.

The fact that the boy choose to run from home for two days instead of relying on her caused her pain and she didn't even know what she should do.

"However Naruto had practically dragged her to where Shinji's was being held and told her to try her best since he had already had his talk with the boy.

"Long time on see." Misato said trying to start the conversation.

"Yeah I guess." Shinji said.

"Do you feel any better after wondering around for a few days?" The commander asked the second child.

"Yes I believe I do for now." Shinji said as he continued to sit shrouded in the darkness of the room.

"Your Eva is on standby, will you pilot it?" Misato asked the melancholy child.

"You're not going to scold me for running away?" Shinji asked the woman who wanted with all her heart to be like a mother of big sister figure to him.

She also felt this way about Rei and Naruto, however Rei was too focused on Naruto and didn't seem to notice her that much.

When it comes to Naruto, he was the one that seemed more like the older brother too all three of them.

"Naruto had said that he was someone that I would come to trust with my life and he wasn't mad when he found out that I was scared of him." Shinji said much to Misato's surprise.

"I want to know if I can feel the same with you and Rei as well, however while I'm out there fighting not only for my life but for the rest of humanity, you are safe underground at headquarters just giving out orders." Shinji tells Misato.

"Rei, Naruto and I are the only ones in real danger out there!" Shinji proclaims as he stands up and turns towards Misato.

Misato turns away from him for a second and sighs, before she walks up to him and takes ahold of his hand.

Come with me for a minute." Misato said as she leads him to and elevator which would take them to Nerv's Geo front down underground.

"Fifteen years ago during the second impact, half of the world's population was wiped out." Misato began explaining to the child.

"If we allow the angels to bring about the third impact now, the human race will not survive not a single soul." Misato informs Shinji.

"I already know all this, I don't need to hear it again." Shinji said.

"If an angel ever manage to make it passed our defense and makes its way all the way down here to level triple E, this whole place is set to automatically self-destruct." Misato informed the boy.

"Even if it cost us our own lives to kill the angel, we will prevent the third impact from happening." Misato declared.

"Every man and woman in this organization is prepared to pay that price."

They soon make it to central dogma and come across a large door. Misato then uses her key card to open the door and Shinji was almost speechless at what he saw within the large room.

"There at the center of the room nailed and speared to a cross-like structure was a white behemoth who was missing the lower part of its body and wore a weird-ass mask with two eye holes showing off her soulless red-eyes.

"What the hell is that? It can't be… an Eva?" Shinji asked Misato while watching as little legs and feet that, while as white as the being looked to belong to humans started swinging around.

Shinji also noticed that LCL was pouring from the bottom of it into a pool of LCL under it.

"No… what you're seeing is the origin of all life on this planet, as well as the key to its end, the second angel Lilith." Misato informed Shinji much to his surprise.

"Lilith…? Shinji asked.

"That's right and it's the trigger that will set off the third impact, we have to protect Lilith, that is what the Eva's are for and one is something only you can do." Misato informs him.

In other words we have entrusted the fate of the world and all of mankind in you, the Eva and Naruto and Rei." Misato said.

"But that's so much to ask of us, and however I now understand what Naruto was saying." Shinji said.

ANaruto clone smiled as he heard what Shinji said from his place hidden within the shadows.

"The boss will be pleased when he hears this." The clone states before disappearing in a puff of smoke.

**(Ramiel)**

"It's time now, for the extermination of all lilin, so that we can claim this planet that was taken from us by those worthless creatures." Ramiel proclaims as his human shell starts glowing

Suddenly, the 6th angel started to grow and transform into this gigantic floating crystalline octahedron.

The surface of Ramiel is blue and highly reflective.

While letting out a loud screech, Ramiel rose into the sky and floated towards Nerv, it mission eradication of the lilin race.

**End**

**Wow a lot of interesting things happened in this chapter.**

**Shinji has found his resolve to fight, Rei is starting to show more emotions like amusement and a little happiness at the fact that a member of the opposite sex has an interest in her.**

**There are many other important things that happened as well so I expect a lot of reviews.**

**Read, Review and subscribe if you've haven't.**

**See you all next time**

**Juubi Ookami Sighing out **


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